1. Pre-requisites and installation¶
1.1. Pre-requisites¶
To fully use the INCAWrapper you need to install the following software:
Python (>=3.8)
matlab (>2022b this allows installation of the matlabengine package through pip)
matlab Statistics and Machine Learning Toolbox and Optimization Toolbox (installed through the matlab Add-on manager)
INCA software (https://mfa.vueinnovations.com/)
Both matlab and INCA are commercial software and the each user needs to acquire a license. The INCAWrapper can be used without a matlab or INCA license, but will not be able to run INCA (See below).
matlab: Get a free academic licence and install MATLAB from https://www.mathworks.com. Then, install the engine API following the guide provided under this link. In brief, you will have to go to your MATLAB root folder (find your installation and open that folder) and go to “/extern/engines/python” and run “python setup.py install” from the command line.
INCA: INCA (Isotopomer Network Compartmental Analysis) is a MATLAB-based software package for isotopomer network modeling and metabolic flux analysis.” You can read more about it in Young, 2014. If you are in academia, you can get a free academic licence for INCA from the Vanderbilt University website (the second option is the relevant one) and install it. Find the path to the base directory of your INCA installation, you will need it later.
1.2. How to install¶
INCAWrapper requires Python. The recommended installation method is pip.
pip install incawrapper[matlab]
Alternatively, you can download the source code from GitHub and install it manually.
git clone github.com/biosustain/incawrapper
cd incawrapper
pip install incawrapper[matlab]
1.3. Use without matlab¶
The INCAWrapper can be used analyse INCA output files (.mat) without matlab. In that case install the package without the matlab using the following command:
pip install incawrapper
With this installation the INCAWrapper can read INCA output files and to create a INCA scripts, but will not be able to run INCA.